Can Probiotics Help Prevent Babies from Developing Food Allergies?

This post was written in partnership with Persephone. All opinions are my own.

Food allergies in babies and toddlers are on the rise, leaving many of us (parents and healthcare providers alike) wondering if there’s anything we can do to help lower our children’s risk.

While there’s no single magic solution, one area of research that’s generating a lot of buzz is the use of probiotics during infancy. 

New studies are uncovering the critical role that the gut microbiome plays in shaping immune system development, and how probiotics might help prevent food allergies from developing in the first place.

As a pediatric dietitian, I’ve been closely following this research and am excited to share some of the latest findings. My goal in this post is to provide insights for you on what we currently know about probiotics, gut health, and food allergies, and to discuss some of the most exciting and recent studies revealing insights into prevention, so that you can make informed decisions about managing your baby’s health, based on the latest evidence.

The Gut-Immune Connection in Early Life

The first 1,000 days of life (from pregnancy through toddlerhood) are a critical window for immune and gut development. Babies are born with a relatively “naïve” immune system, and the microbes that colonize their intestines during infancy help train the body to tell the difference between harmless foods and potential threats.

The gut microbiome, made up of trillions of bacteria that reside in the digestive tract, plays a significant role in this training process. It seems that when the gut is rich in beneficial bacteria, it can help the immune system develop tolerance to foods such as milk, peanuts, and eggs. 

On the other hand, when the gut microbiome is disrupted early in life, as can occur after antibiotic use, the risk of food allergies can increase. Research suggests that certain probiotics may help restore a healthy balance of gut bacteria and support the immune system in building tolerance rather than reacting via allergy development.

What Research Says About Probiotics and Food Allergies

Probiotics are live, friendly microorganisms that, when administered in adequate amounts, provide beneficial effects to the host and may support a healthy gut microbiome. Researchers have been investigating whether giving specific probiotics during infancy may reduce the risk of food allergies, and the results are promising, although not yet conclusive.

The My Baby Biome Study is one of the largest and most comprehensive projects to date, looking at the infant gut microbiome. Researchers have found that the makeup of gut bacteria in early life strongly predicts the likelihood of developing food allergies, eczema, and asthma later in life.

Some of the key findings from this study and others include the following:

• Infant gut composition matters: Babies who later develop food allergies often have fewer Bifidobacterium and Lactobacillus species early in life.

• Probiotic supplementation may be beneficial: Studies have shown that specific strains of probiotics can enhance gut diversity and support immune balance, potentially improving tolerance to allergenic foods such as milk, eggs, and peanuts.

• Timing is key: The protective effects of probiotics may be strongest when given ideally during the first year or two of life, when the immune system is rapidly developing.

Beyond allergy prevention, probiotics for infants may also support digestive comfort (such as reduced gas, constipation, or diarrhea), immune system balance, reduced colic, and skin health, with some studies linking probiotic use to lower rates of eczema. 

Although more research is needed, these potential benefits make probiotics an intriguing addition to infant nutrition strategies, especially when we consider how well-tolerated they are in most infants.

Introducing Persephone: A New Infant and Toddler Synbiotic 

One of the most exciting developments in the probiotic world comes from the My Baby Biome Study. This research laid the foundation for the development of Persephone, a new synbiotic (probiotics + prebiotics) designed to restore the protective bacteria that healthy babies naturally have—key microbes that are often missing in infants today and are linked to lower allergy risk and stronger immune support.

Persephone is now being evaluated in the ARTEMIS clinical trial, which is focused on understanding how this synbiotic supports the developing infant gut. As a next step, our research will also explore how restoring these early-life microbes may help reduce the risk of immune-related conditions, such as food allergies.

What Makes Persephone Unique?

Researchers emphasize that not all probiotics are equal and the benefits depend on the strain, dose, and duration of supplementation. Most of the available probiotics marketed for infants aren’t actually made with the specific needs of babies in mind, nor are they backed by the latest research. Here are some of the reasons why Persephone’s probiotic is unique.

• SYNERGISTIC SYNBIOTIC: Unlike most probiotic and synbiotic products, Persephone is actually a science-backed, synergistic synbiotic, meaning that it contains both probiotic bacteria and the specific prebiotic fibers that feed those specific probiotic strains and help them thrive. The prebiotics used are human milk oligosaccharides (HMOs) (i.e., the same prebiotics found in breast milk).

• 4 KEYSTONE PROBIOTIC STRAINS: Persephone contains 4 targeted strains of beneficial bacteria linked to immune tolerance, including two proprietary Bifidobacterium infantis species (the keystone species that is disappearing from modern babies’ guts), and Bifidobacterium breve and Bifidobacterium longum, which also play essential supporting roles in early gut development and during the transition to solid foods.

• WHY THESE STRAINS? The My Baby Biome Study found that 9 out of 10 U.S. infants (especially c-section babies, like my three) have little to no Bifidobacterium in their guts. This matters because babies in the study with low levels were about 3 times more likely to develop allergic conditions (like food allergies!) by age two, and higher levels were linked to a nearly 5-fold reduction in allergy risk. 

• THIRD-PARTY TESTING: Every batch undergoes extensive third-party testing by labs such as Eurofins and Light Labs to ensure safety and purity.

• CLEAN LABEL-CERTIFIED: It is certified by the Clean Label Project’s First 1000 Days Promise, a program that sets strict standards for contaminants in products intended for infants and young children. This level of testing and quality assurance is something I always look for as a pediatric dietitian when recommending supplements for babies and toddlers!

Practical Tips for Starting Your Baby on a Synbiotic 

Personally, one of the reasons I love Persephone is how easy it is to use and build into the daily routine. It comes in individual sachets of slightly sweet and pleasant-tasting powder that dissolves quickly and easily into a bottle of formula or breast milk, or even a spoonful of baby food once your little one starts solids. If you are exclusively breastfeeding, you can mix it into a paste with a bit of water and apply it directly to a pacifier or your nipple before a feed.

When you first start offering Persephone to your baby, many families find it’s best to go “low and slow,” to give the baby’s system time to adjust. In other words, offer just a pinch of powder for the first 1-2 days, then half a packet on days 3-4, and offer a full packet on day 5 and on each day going forward.  

After your baby’s first birthday, you can transition your baby to Persephone’s toddler synbiotic, which is designed to support digestive health, immune system development, and even brain development in little ones ages 1-3. 

**It is important to note that if your baby was born prematurely, or has a weakened immune system or medical condition, it’s best to check with your pediatrician before starting any supplement, including a probiotic or synbiotic. 

The Bottom Line

Probiotics won’t guarantee that your baby will avoid food allergies, but the latest research suggests they may support gut health and immune tolerance in ways that reduce risk. 

If you’re considering probiotics for your baby, talk with your pediatrician or registered dietitian about whether it is right for your child.

And if you’re preparing to start solids, remember that early and consistent exposure to allergenic foods, like peanuts, eggs, and yogurt, is still the most well-established strategy for reducing allergy risk. Probiotics may prove to be an important piece of the puzzle, but they work best in conjunction with other evidence-based feeding practices.

Want to learn more? 

• FREE WEBINAR ON THE GUT + ALLERGY CONNECTION: I’ll be joining a panel of experts, along with Persephone’s lead researcher, in a FREE webinar about the gut + allergy connection on November 12th: Register here. 

• TRY PERSEPHONE: Visit Persephone’s website to learn more and/or order your first box.

• FOOD ALLERGY PREVENTION GUIDE & COOKBOOK: If you're looking for step-by-step help with starting solids, family-friendly recipes, and the latest research on food allergy prevention, consider my new cookbook and guide to starting solids and introducing allergens. It’s designed to make the mental load of feeding your baby both easier and more enjoyable for your whole family.

Thanks for reading!